amr_curation
amr_curation copied to clipboard
arpcard
BioF class B2 beta-lactamase should get a PFM allele number ?
A paper describing a new class B2 beta-lactamase named BioF has just come out ("BioF is a novel B2 metallo-β-lactamase from Pseudomonas sp. isolated from an on-farm biopurification system", Environ Microbiol. 2021 Nov 1. doi: 10.1111/1462-2920.15822.)
However, this enzyme clearly belongs to the PFM family, as shown in Fig. 3 from the paper (see attached image). It has ~96% sequence identity with PFM-2 and PFM-3, and 90% with PFM-1. In these conditions, I would suggest to assign a PFM allele number for BioF.
Additionally, there are five other PFM-like sequences currently deposited in GenBank (see below the sequence alignment and the percent identity matrix), for which allele numbers may also be assigned to avoid confusion in the future.
PMV25217.1|PFM-like-3| MKLSSILSALSMACVTCQVIANDTNLTLTHFKGPLYIVEDKEYVQENSMVYIGAQNITII 60
QDC33502.1|PFM-1| MKVINILSAVSMFCITCQALANDINLTLTHFKGPLYIVEDKEYVQENSMVYIGAQDITII 60
OAE14554.1|BioF| MKLINILSVISLACITSQVFANKSDLTLTHFKGPLYIVEDKEYVQENSMVYVGEQHITVI 60
WP_053221259.1|PFM-like-2| MKLINILSAISLACITSQVFANQSDLTLTNFKGPLYIVEDKEYVQENSMVYIGEQHITVI 60
KRP45299.1|PFM-2| MKLINILSAISLACITSQVFANQSDLTLIHFKGPLYIVEDKEYVQENSMVYIGEQHITVI 60
WP_223023558.1|PFM-like-5| MKLINILSAISLACITSQVFANQSDLTLSHFKGPLYIVEDKEYVQENSMVYIGEQHITVI 60
WP_050516231.1|PFM-like-1| MKLINILSAISLACITSQVFANQSDLTLTHFKGPLYIVEDKEYVQENSMVYIGAQHITVI 60
QGJ02507.1|PFM-3| MKLINILSAISLACITSQVFANQSDLTLTHFKGPLYVVEDKEYVQENSMVYVGAQHITVI 60
WP_202691781.1|PFM-like-4| MKLINILSAISLACITSQVFANQSDLTLTHFKGQLYIVEDKEYVQENSMVYIGAQHITVI 60
**: .***.:*: *:*.*.:**. :*** :*** **:**************:* *.**:*
PMV25217.1|PFM-like-3| GATWTPATAEKLEQEIRRVSPLPIKDVINTNYHTDRAGGNAYWKKRGASIVSTQMTYDLE 120
QDC33502.1|PFM-1| GATWTPATAEKLEQEIRKISSLPIKEVINTNYHTDRAGGNAYWKKLGASIVSTQMTYDLE 120
OAE14554.1|BioF| GATWTPATAEKLEQEIRKISPLPIKEVINTNYHTDRAGGNAYWKKLGASIVSTQMTYDLE 120
WP_053221259.1|PFM-like-2| GATWTPATAEKLEQEIRKVSPLPIKEVINTNYHTDRAGGNAYWRELGASIVSTQLTYDLE 120
KRP45299.1|PFM-2| GATWTPATAEKLEQEIRKISPLPIKEVINTNYHTDRAGGNAYWRKLGASIVSTQMTYDLE 120
WP_223023558.1|PFM-like-5| GATWTPATAEKLEQEIRKISPLPIKEVINTNYHTDRAGGNAYWKKLGASIVSTQMTYDLE 120
WP_050516231.1|PFM-like-1| GATWTPATAEKLEQEIRKISPLPIKEVINTNYHTDRAGGNAYWKELGASIVSTQMTYDLE 120
QGJ02507.1|PFM-3| GATWTPATAEKLEQEIRKISPLPIKEVINTNYHTDRAGGNAYWKKLGASIVSTQMTYDLE 120
WP_202691781.1|PFM-like-4| GATWTPATAEKLEQEIRKISPLPIKEVINTNYHTDRAGGNAYWKKLGASIVSTQMTYDLE 120
*****************::* ****:*****************:: ********:*****
PMV25217.1|PFM-like-3| KSQWRSIVDFTRQGMEHFPVLEQSLPDKVHPGDFTLQNGNVRAMYLGAAHTEDGIFVYFP 180
QDC33502.1|PFM-1| KTNWRGIVDFTRQGMEHYPVLEQSLPDQVYPGDFALQNGHVRALYLGASHTEDGIFVYFP 180
OAE14554.1|BioF| KSQWRSIVDFTRQGMEHYPILEQSLPDQVYPGNFDLQNGHVRALYLGASHTEDGIFVYFP 180
WP_053221259.1|PFM-like-2| KSQWRSIVDFTRQGMEHYPVLEQSLPDQVYPGDFALQNGHVRALYLGASHTEDGIFVYFP 180
KRP45299.1|PFM-2| KSQWRSIVDFTRQGMEHYPVLEQSLPDQVYPGDFALQNGHVRALYLGASHTEDGIFVYFP 180
WP_223023558.1|PFM-like-5| KSQWRSIVDFTRQGMEHYPVLEQSLPDQVYPGDFALQNGHVRALYLGASHTEDGIFVYFP 180
WP_050516231.1|PFM-like-1| KSQWRSIVDFTRQGMEHYPVLEQSLPDQVYPGDFALQSGHVRALYLGASHTEDGIFVYFP 180
QGJ02507.1|PFM-3| KSQWRSIVDFTRQGMEHYPVLEQSLPDQVYPGDFALQNGHVRALYLGASHTEDGIFVYFP 180
WP_202691781.1|PFM-like-4| KSQWRSIVDFTRQGMEHYPVLEQSLPDQVYPGDFALQNGHVRALYLGASHTEDGIFVYFP 180
*::**.***********:*:*******:*:**:* **.*:***:****:***********
PMV25217.1|PFM-like-3| EERVLYGNCILKEKLGNMTFANRTEYPKTLKKLQGLIDSGELPVDAIIAGHNSPIQGVEL 240
QDC33502.1|PFM-1| EERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQGLIRSGELSVEAIIAGHNSPIQSVEL 240
OAE14554.1|BioF| EERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQGLIRSGELPVEAIIAGHNSPIQNVEL 240
WP_053221259.1|PFM-like-2| EERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQGLISSGELPVETIIAGHNSPIQSVEL 240
KRP45299.1|PFM-2| EERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQGLISSGELPVEAIIAGHNSPIQSVEL 240
WP_223023558.1|PFM-like-5| EERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQGLISSGELPVEAIIAGHNSPIQSVEL 240
WP_050516231.1|PFM-like-1| EERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQVLISSGELPVETIIAGHNSPIQSVEL 240
QGJ02507.1|PFM-3| EERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQGLISSGELPVEAIIAGHNSPIQSVEL 240
WP_202691781.1|PFM-like-4| EERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQGLISSGELPVETIIAGHNSPIQSVEL 240
***********************:********** ** **** *::**********.***
PMV25217.1|PFM-like-3| IDQYLNLLEHDKH 253
QDC33502.1|PFM-1| IDHYLNLLEHGEQ 253
OAE14554.1|BioF| IDHYLTLLEHGEQ 253
WP_053221259.1|PFM-like-2| IDHYLNLLEHGEQ 253
KRP45299.1|PFM-2| IDHYLNLLEHGEQ 253
WP_223023558.1|PFM-like-5| IDHYLNLLEHGEQ 253
WP_050516231.1|PFM-like-1| IDHYLNLLEHGEQ 253
QGJ02507.1|PFM-3| IDHYLNLLEHGEQ 253
WP_202691781.1|PFM-like-4| IDHYLNLLEHGEQ 253
**:**.****.::
1: PMV25217.1|PFM-like-3| 100.00 86.56 85.38 85.77 86.56 86.96 86.17 86.96 86.96
2: QDC33502.1|PFM-1| 86.56 100.00 90.12 90.12 91.70 92.09 91.30 92.09 92.09
3: OAE14554.1|BioF| 85.38 90.12 100.00 94.07 95.65 96.05 94.47 96.05 95.26
4: WP_053221259.1|PFM-like-2| 85.77 90.12 94.07 100.00 97.63 97.23 97.23 96.44 97.23
5: KRP45299.1|PFM-2| 86.56 91.70 95.65 97.63 100.00 99.21 97.23 98.02 98.02
6: WP_223023558.1|PFM-like-5| 86.96 92.09 96.05 97.23 99.21 100.00 97.63 98.42 98.42
7: WP_050516231.1|PFM-like-1| 86.17 91.30 94.47 97.23 97.23 97.63 100.00 97.63 98.42
8: QGJ02507.1|PFM-3| 86.96 92.09 96.05 96.44 98.02 98.42 97.63 100.00 98.42
9: WP_202691781.1|PFM-like-4| 86.96 92.09 95.26 97.23 98.02 98.42 98.42 98.42 100.00
The authors of the paper have contacted me et they agreed with the use of PFM-4 for this enzyme from now on. @danielhhaft and @agmcarthur, can you please add this enzyme to NCBI's AMRDB and add PFM-4 as a synonym for CARD entry 45492, respectively? Thanks !
PFM-4 as a synonym for BioF has been curated in CARD and will appear in the next release. We will defer to NCBI on whether this becomes the official name.
Thank you Bogdan and Andrew. PFM-4 will be official at NCBI. BioF can be an alternate name. I have just made the change, but it may be a little while before the next release.
